Intergenic Non-Switch Immunoglobulin Translocations Are Frequently Observed in Genomically Unstable MM

Multiple myeloma (MM) is a B cell malignancy involving terminally differentiated plasma cells that is often initially driven by translocations of the IGHgene at 14q32 (tIGH, observed in ~35% of patients). It is believed that the main cause of tIGH is activation-induced cytidine deaminase (AID), which is a protein that mediates antibody class switching. This is based on data from MM cell lines, where tIGH is located most often in breakpoints in the switch regions. However, it can also be in the VDJ regions, which implicates dysregulated VDJ recombination. To fully understand the mechanisms behind tIGH, we must first fully catalog the spectrum of these translocations and assess their association with other genomic features.

Here, we analyzed deep whole-genome sequencing from 1257 newly diagnosed patients enrolled in the IFM or DFCI trials as well as the MMRF cohort. In addition, targeted sequencing data were collected from 4078 patients in the IFM network. tIGH breakpoints were classified according to their overlap with the switch, 3' regulatory (3'RR) or VDJ regions. If a breakpoint did not overlap with any of these regions, it was considered "intergenic". Overall, we identified tIGH in 38% of patients, and among all tIGH breakpoints, switch region translocations were the most frequent (59.5%) followed by 24.8% in the VDJ regions, 12% in intergenic regions and 3.7% in the 3'RR.

We next looked at how common translocations in MM were related to various breakpoint locations. t(4;14) occurred almost exclusively in switch regions (95.7%, 95% CI 92.7-97.7%, p value < 2.2e-16). For other translocations (t(6;14), t(11;14), t(14;16), t(14;20)), tIGH tended to be in the switch regions (max 62%) but they were also present in VDJ regions (range 12.6 to 30.9%). On the other hand, for MYC-targeting translocations (t[8;14]), the most common breakpoints were in intergenic (37.8%, 95%CI 28.1-48.4%, p value = 9.5e-11) regions and the 3'RR.

To investigate the mechanisms that translocate IGHto intergenic regions, we first searched for homology and found that intergenic breakpoint hotspots have a high sequence similarity between each other and IgHG1/2/3/4 (cosine distance > 0.80) unlike IgHA and IgHM. Because AID is involved in somatic hypermutation, we next investigated the mutational load of tIGH and found a significant increase in mutations (Kruskal-Wallis p value = 0.03) from VDJ to switch to intergenic patients. However, the intergenic group had significantly lower AID-related mutations on both an absolute (t test p value = 0.007) and normalized (t test p value = 0.002) scale. In addition, the intergenic group had increased genomic instability, as assessed by CNA segmentation and the percentage of the genome that was either amplified or deleted (Wilcoxon p value = 0.048). Furthermore, genes involved in genome instability and class switch-associated genes, like BLM and TP53BP1, were only mutated in the intergenic group. There were no KRAS mutations in the intergenic group (p value = 0.011), whereas BRAFmutations were much more common (p value=0.008, OR=17.3).

Overall, our study indicates that multiple factors contribute to tIGH and these factors correlate to MM subgroups. tIGH in patients with t(4;14) is clearly associated with faulty class switching, likely caused by AID, whereas patients with other translocations appear to have multiple potential mechanisms. Interestingly, even within the MM subgroups, those patients with tIGH in an intergenic region have increased hypodiploidy frequency, implicating a mechanism that also plays a role in genomic stability.

Munshi:GSK: Consultancy; Janssen: Consultancy; Amgen: Consultancy; Takeda Oncology: Consultancy; Bristol-Myers Squibb: Consultancy; Abbvie: Consultancy; Pfizer: Consultancy; Novartis: Consultancy; Adaptive Biotechnology: Consultancy; Oncopep: Consultancy, Current equity holder in publicly-traded company, Other: scientific founder, Patents & Royalties; Karyopharm: Consultancy; Celgene: Consultancy; Legend: Consultancy.